Related papers: Reactive Molecular Dynamics study on the first ste…
We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte…
Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to reveal the effect of hydroxyl radicals produced by the secondary effect of radiation. Previous studies address the problem…
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy, radio-biology and critical to space-projects. In this study we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic…
This paper describes the model for DNA in MATLAB taking into account all of component atoms. In this model, it is possible to generate sequences with length 10000 basis pairs available for introducing all types of sequences. Once the…
It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing…
In order to study the molecular damage induced in the form of single-strand and double-strand breaks by the ionizing radiation at the DNA level, Geant4-DNA Monte Carlo simulation code for complete transportation of primary protons and other…
This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The analysis and assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms…
Ion-induced DNA damage is an important effect underlying ion-beam cancer therapy. This paper introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically, it is demonstrated how single-…
This work establishes a protocol to study via Molecular Dynamics simulation the degradation of Per-and Polyfluoroalkyl Substances (PFAS) in water by hydroxyl radical. To achieve this, molecular dynamics simulations are carried out, using…
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and…
Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of…
We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy. We…
The elucidation of fundamental mechanisms underlying ion-induced radiation damage of biological systems is crucial for the advancement of radiotherapy with ion beams and for radiation protection in space. The study of ion-induced biodamage…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA…
The hydroxyl radical is the primary reactive oxygen species produced by the radiolysis of water, and is a significant source of radiation damage to living organisms. Mobility of the hydroxyl radical at low temperatures and/or high pressures…
Energetic ions lose their energy in tissue mainly by ionising its molecules. This produces secondary electrons which transport this energy radially away from the ion path. The ranges of most of these electrons do not exceed a few…
We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $\beta$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the…
The development of intense high-energy radiation sources and the improvement of techniques for detecting charged fragments have made possible experiments on multiple ionization of a molecule with registration of the momentum and charge of…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…